Computational screen for spliceosomal RNA genes aids in defining the phylogenetic distribution of major and minor spliceosomal components.
Computational screen for spliceosomal RNA genes aids in defining the phylogenetic distribution of major and minor spliceosomal components.
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DOI：
10.1093/nar/gkn142
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发表时间：
2008-05
影响因子：
14.9
通讯作者：
Samuelsson T
中科院分区：
文献类型：
--
作者：
Dávila López M;Rosenblad MA;Samuelsson T
剪接体的RNA分子对于真核前体mRNA剪接过程中的特异性和催化作用至关重要。为了研究这些RNA的进化和系统发育分布，我们分析了149个真核生物基因组，代表了广泛的系统发育组。使用高灵敏度的局部比对方法和配置文件的HSP70与协方差模型相结合，预测RNA。结果提供了最全面的看法，迄今为止的系统发育分布的剪接体RNA。在许多系统发育组中预测了RNA，这些RNA以前没有报道过。例子是RNA的主要（U2型）剪接体在所有真菌谱系，在较低的后生动物和许多原生动物。我们还确定了次要（U12型）剪接体U11和U6atac RNA卡氏阿米巴，其中U12剪接体RNA以及次要内含子最近报道。此外，小剪接体特异性RNA被确定在一些系统发育组，以前没有观察到这样的RNA，包括线虫旋毛虫，黏液霉菌多头绒泡菌和真菌谱系接合菌门和壶菌门。U12型RNA基因分布的详细地图支持小剪接体的早期起源，并指出在进化过程中它丢失的一些场合。
The RNA molecules of the spliceosome are critical for specificity and catalysis during splicing of eukaryotic pre-mRNA. In order to examine the evolution and phylogenetic distribution of these RNAs, we analyzed 149 eukaryotic genomes representing a broad range of phylogenetic groups. RNAs were predicted using high-sensitivity local alignment methods and profile HMMs in combination with covariance models. The results provide the most comprehensive view so far of the phylogenetic distribution of spliceosomal RNAs. RNAs were predicted in many phylogenetic groups where these RNA were not previously reported. Examples are RNAs of the major (U2-type) spliceosome in all fungal lineages, in lower metazoa and many protozoa. We also identified the minor (U12-type) spliceosomal U11 and U6atac RNAs in Acanthamoeba castellanii, where U12 spliceosomal RNA as well as minor introns were reported recently. In addition, minor-spliceosome-specific RNAs were identified in a number of phylogenetic groups where previously such RNAs were not observed, including the nematode Trichinella spiralis, the slime mold Physarum polycephalum and the fungal lineages Zygomycota and Chytridiomycota. The detailed map of the distribution of the U12-type RNA genes supports an early origin of the minor spliceosome and points to a number of occasions during evolution where it was lost.
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影响因子：
64.8
作者：
Russell, Anthony G.;Charette, J. Michael;Gray, Michael W.
通讯作者：
Gray, Michael W.
影响因子：
3.4
作者：
Russell AG;Shutt TE;Watkins RF;Gray MW
通讯作者：
Gray MW
DOI：
10.1073/pnas.042700299
发表时间：
2002-03-19
影响因子：
11.1
作者：
Nixon, JEJ;Wang, A;Samuelson, J
通讯作者：
Samuelson, J
影响因子：
4.5
作者：
Incorvaia, R;Padgett, RA
通讯作者：
Padgett, RA
影响因子：
14.9
作者：
Rozhdestvensky, TS;Tang, TH;Hüttenhofer, A
通讯作者：
Hüttenhofer, A